Key points for Chapter 61. Definitions: topoisomerase, ribozyme, do

uble helix, DNA denaturation, Tm, linking number, pseudoknot.

2. What are the structural differences between DNA and RNA? How the structural properties of DNA and RNA determine their distinct biological functions.

Key points for Chapter 71. Definitions: nucleosome, gene

density, core histones (structure and function), Nucleosome remodeling complexes

2. Describe the important functions of packing of DNA into chromosome.

3. Why genes make up only a small proportion of the eukaryotic genome.

Key points for Chapter 7

4. Briefly describe roles of three critical DNA elements important for chromosome duplication & segregation

5. Briefly describe how the higher-order chromatin structure is formed

Key points for Chapter 81. Definitions: replication fork, leading strand,

lagging strand, Okazaki fragment, processivity, proofreading exonuclease, replisome, pre-replicative complexes (pre-RCs)

2. Describe the function and mechanism of DNA polymerase.

3. Describe DNA replication process and proteins involved at a replication fork.

Key points for Chapter 84. How is the DNA replication tightly

controlled in E. coli and in eukaryotic cells?

5. What is the end replication problem? how does cell resolve the problem?

Key points for Chapter 91. Definitions: replication errors,

spontaneous DNA damage, DNA mutations, double-strand break (DSB) repair pathway.

2. How does the mismatch repair system accurately detect, remove and repair the mismatch resulting from inaccurate replication?

3. What are the environmental factors that cause DNA damage?

Key points for Chapter 94. How could a DNA damage be converted to

DNA mutation? 5. What are the mechanisms to repair a DNA

damage? Describes how base excision and repair and nucleotide excision repair work?

6. What is translesion DNA synthesis? Why it is important?

Key points for Chapter 10

1. Definitions: Mating-type switching, gene conversion, Holliday junction

2. Compare the two models for homologous recombination, which model finds more evidence?

3. Describe RecBCD pathway and protein involved in bacteria, and the function of the eukaryotic homologue Spo11, MRX and Dmc1

Key points for Chapter 111. Conservative site-specific

recombination (CSSR): definition, consequence, mechanism and examples.

2. Transposon and transposition: definitions, consequence, basic structural feature of three principle classes of transposable elements, and the mechanism of viral-like retrotransposons/retroviruses

Key points for Chapter 121. The central dogma,

2. Transposon and transposition: definitions, consequence, basic structural feature of three principle classes of transposable elements, and the mechanism of viral-like retrotransposons/retroviruses

1. RNA polymerases (RNAP, 真核和原核的异同 ) and transcription cycle

2. Transcription cycle in bacteria: Initiation: (1) promoters and promoter recogniti

on by factor (4 domains) and CTD. (2) Transition from the closed complex to the open complex. (3) abortive initiation.

Elongation and proofreading by RNAPTermination: Rho-independent and Rho-depend

ent mechanism

Key points of chapter 12

3. Transcription cycle in eukaryotes: ---RNAP II transcriptionInitiation: (1)Promoter and its recognition by GT

F, (2) Assembly of the pre-initiation complex, (3) Initiation in vivo requires additional proteins____

Elongation: (1) phosphorylation of the CTD tail of RNAP II, shedding most of its initiation factors, and recruiting factors for elongation and RNA processing. (2) How RNA processing is coupled with transcription?

Polyadenylation and termination---RNAP I and III transcriptionGTFs and promoter recognition

Definitions: exons, introns, RNA splicing, spliceosome; alternative RNA splicing, exonic splicing enhancer, SR proteins; trans-splicing; alternative spliceosome; RNA editing, ADAR enzyme, guild RNAs

• The chemical reaction of RNA splicing• Describe the splicing pathway

conducted by dynamic spliceosome assembly

• Self-splicing introns and chemical reactions

• How alternative splicing is regulated?

Key points of chapter 13

1. The main challenge of translation and the solution

2. The structure and function of four components of the translation machinery.

3. Translation initiation, elongation and termination ( 具体过程和翻译因子的作用 )

4. The mRNA and protein stability dependent on translation ( 生物学问题是什么，怎么解决的 )

Key points of chapter 14

Definitions: codon, degeneracy, synonyms, missense mutation, nonsense mutation, frameshift mutation, suppressor gene

• What is the wobble concept? • What are the three rules governing the g

enetic code? • What are the benefits of the code univer

sality (P475)?

Key points of chapter 15

Key points of chapter 16-171. Principles of gene regulation. (1) The targ

eted gene expression events; (2) the mechanisms: by recruitment/exclusion or allostery

2. Regulation in bacteria---transcription initiation : the lac operon, alt

ernative factors, NtrC, MerR, Gal rep, araBAD operon

---after transcription initiation: the trp operon, riboswitch, regulation of the synthesis of ribosomal proteins

3. Regulation in eukaryotes--- Definitions: regulatory sequences, enhancers,

insulators, gene silencing, ChIP, two hybrid assay, LCR,

--- Describe the similarity and differences of regulation between eukaryotes and prokaryote

--- Describe the DNA binding domains and activating regions that eukaryotic activators commonly use.

Regulation at transcription initiation: ---Describe the two ways that eukaryotic activat

ors recruit polymerase.

---How signals are integrated by the function of activators (F17-14)? Give two examples.

---Describe the ways in which eukaryotic repressors work (F17-19)

---Use an example to illustrate that signals are often communicated to transcription regulators through signal transduction pathways (F17-21)

Regulation after transcription initiation:--- Use an example to illustrate regulation of alte

rnative mRNA splicing (F17-28)RNA in gene regulation---Describe the production pathway and the func

tion of siRNA and microRNA

Key points of chapter 19Definitions: cloning vector, expression vector; shotgun s

equencing, comparative genomics, proteomics, mass spectometry (MS); restriction endonuclease, Northern hybridization, southern hybridization, Western blot, PCR; affinity chromatography, gel filtration chromatography, ion exchange chromatography, SDS PAGE.

1. How to clone a gene, to screen for the recombinant plasmid-containing colonies, to express a gene, and to purify an encoded protein?

2. How to create a genomic DNA and a cDNA library?